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  • 1
    Online Resource
    Online Resource
    Valuation of Genomic-Enhanced Expected Progeny Differences in Bull Purchasing
    Cambridge University Press (CUP) ; 2022
    In:  Journal of Agricultural and Applied Economics Vol. 54, No. 4 ( 2022-11), p. 713-722
    Details
    In: Journal of Agricultural and Applied Economics, Cambridge University Press (CUP), Vol. 54, No. 4 ( 2022-11), p. 713-722
    Abstract: We estimate a hedonic pricing model to determine producers’ value for bull expected progeny differences (EPDs), genomic-enhanced EPDs, and phenotypic traits. Birth weight EPD, ribeye area EPD, sale weight, age, frame score, and other factors had a statistically significant impact on bull prices. GE-EPDs were not associated with a change in the bull sales prices expect for weaned calf value and birth weight EPDs. Including weaned calf value and GE-EPDs in a bull hedonic pricing model provides a unique contribution. The results from this work will inform educational programming for bull purchasers on using new economic selection indices and GE-EPDs.
    Type of Medium: Online Resource
    ISSN: 1074-0708 , 2056-7405
    URL: Article
    DOI: 10.1017/aae.2022.36
    Language: English
    Publisher: Cambridge University Press (CUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2141115-3
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  • 2
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    Predicting Seedstock Bull Prices: Does Information Matter?
    Cambridge University Press (CUP) ; 2023
    In:  Journal of Agricultural and Applied Economics Vol. 55, No. 2 ( 2023-05), p. 341-357
    Details
    In: Journal of Agricultural and Applied Economics, Cambridge University Press (CUP), Vol. 55, No. 2 ( 2023-05), p. 341-357
    Abstract: We investigate the role of optimism bias in bull price expectations using incentivized lab-in-the-field experiments with Alabama and Tennessee cattle producers. We develop bull price prediction tasks and reward accurate predictions. We find that the EPD information provision prevents optimism bias from contaminating price expectations in the whole sample. However, we also document that, unlike buyers, sellers are prone to unrealistic optimistic expectations, and our results reveal that optimism bias can be moderated by the type of expected progeny difference information utilized, breed characteristics, and regional differences in cattle operations. We contribute to the literature by documenting the role of behavioral biases.
    Type of Medium: Online Resource
    ISSN: 1074-0708 , 2056-7405
    URL: Article
    DOI: 10.1017/aae.2023.19
    Language: English
    Publisher: Cambridge University Press (CUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2141115-3
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  • 3
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    Genome-wide association and genotype by environment interactions for growth traits in U.S. Red Angus cattle
    Springer Science and Business Media LLC ; 2022
    In:  BMC Genomics Vol. 23, No. 1 ( 2022-07-16)
    Details
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 23, No. 1 ( 2022-07-16)
    Abstract: Genotypic information produced from single nucleotide polymorphism (SNP) arrays has routinely been used to identify genomic regions associated with complex traits in beef and dairy cattle. Herein, we assembled a dataset consisting of 15,815 Red Angus beef cattle distributed across the continental U.S. and a union set of 836,118 imputed SNPs to conduct genome-wide association analyses (GWAA) for growth traits using univariate linear mixed models (LMM); including birth weight, weaning weight, and yearling weight. Genomic relationship matrix heritability estimates were produced for all growth traits, and genotype-by-environment (GxE) interactions were investigated. Results Moderate to high heritabilities with small standard errors were estimated for birth weight (0.51 ± 0.01), weaning weight (0.25 ± 0.01), and yearling weight (0.42 ± 0.01). GWAA revealed 12 pleiotropic QTL (BTA6, BTA14, BTA20) influencing Red Angus birth weight, weaning weight, and yearling weight which met a nominal significance threshold ( P ≤  1e-05) for polygenic traits using 836K imputed SNPs. Moreover, positional candidate genes associated with Red Angus growth traits in this study (i.e., LCORL, LOC782905, NCAPG, HERC6, FAM184B, SLIT2, MMRN1, KCNIP4, CCSER1, GRID2, ARRDC3, PLAG1, IMPAD1, NSMAF, PENK, LOC112449660, MOS, SH3PXD2B, STC2, CPEB4 ) were also previously associated with feed efficiency, growth, and carcass traits in beef cattle. Collectively, 14 significant GxE interactions were also detected, but were less consistent among the investigated traits at a nominal significance threshold ( P ≤  1e-05); with one pleiotropic GxE interaction detected on BTA28 (24 Mb) for Red Angus weaning weight and yearling weight. Conclusions Sixteen well-supported QTL regions detected from the GWAA and GxE GWAA for growth traits (birth weight, weaning weight, yearling weight) in U.S. Red Angus cattle were found to be pleiotropic. Twelve of these pleiotropic QTL were also identified in previous studies focusing on feed efficiency and growth traits in multiple beef breeds and/or their composites. In agreement with other beef cattle GxE studies our results implicate the role of vasodilation, metabolism, and the nervous system in the genetic sensitivity to environmental stress.
    Type of Medium: Online Resource
    ISSN: 1471-2164
    URL: Article
    DOI: 10.1186/s12864-022-08667-6
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2041499-7
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  • 4
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    Exploring genetic variation and population structure in a threatened species, Noturus placidus , with whole-genome sequence data
    Oxford University Press (OUP) ; 2022
    In:  G3 Genes|Genomes|Genetics Vol. 12, No. 4 ( 2022-04-04)
    Details
    In: G3 Genes|Genomes|Genetics, Oxford University Press (OUP), Vol. 12, No. 4 ( 2022-04-04)
    Abstract: The Neosho madtom (Noturus placidus) is a small catfish, generally less than 3 inches in length, unique to the Neosho-Spring River system within the Arkansas River Basin. It was federally listed as threatened in 1990, largely due to habitat loss. For conservation efforts, we generated whole-genome sequence data from 10 Neosho madtom individuals originating from 3 geographically separated populations to evaluate genetic diversity and population structure. A Neosho madtom genome was de novo assembled, and genome size and content were assessed. Single nucleotide polymorphisms were assessed from de Bruijn graphs, and via reference alignment with both the channel catfish (Ictalurus punctatus) reference genome and Neosho madtom reference genome. Principal component analysis and structure analysis indicated weak population structure, suggesting fish from the 3 locations represent a single population. Using a novel method, genome-wide conservation and divergence between the Neosho madtom, channel catfish, and zebrafish (Danio rerio) was assessed by pairwise contig alignment, which demonstrated that genes important to embryonic development frequently had conserved sequences. This research in a threatened species with no previously published genomic resources provides novel genetic information to guide current and future conservation efforts and demonstrates that using whole-genome sequencing provides detailed information of population structure and demography using only a limited number of rare and valuable samples.
    Type of Medium: Online Resource
    ISSN: 2160-1836
    URL: Article
    DOI: 10.1093/g3journal/jkac046
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2629978-1
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  • 5
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    101 National Center for Applied Reproduction and Genomics (NCARG) evaluates accuracy of genomic prediction in commercial Angus cattle
    Oxford University Press (OUP) ; 2019
    In:  Journal of Animal Science Vol. 97, No. Supplement_3 ( 2019-12-05), p. 84-84
    Details
    In: Journal of Animal Science, Oxford University Press (OUP), Vol. 97, No. Supplement_3 ( 2019-12-05), p. 84-84
    Abstract: One of the goals of the National Center of Applied Reproduction and Genomics (NCARG) is to demonstrate in real-world settings the potential of new technologies. To this end, we evaluated the predictive ability of the Zoetis GeneMax Advantage genomic prediction. The GeneMax Advantage test analyzes tens of thousands of single nucleotide polymorphisms (SNP) to predict the genetic potential of a commercial Angus female. Genetic predictions are provided for Calving Ease Maternal, Weaning Weight, Heifer Pregnancy, Milk, Mature Weight, Dry Matter Intake, Carcass Weight, Marbling, and Yield. Indices of economically important traits are estimated on an index score (1–100 scale) and are reported in three indices; Cow Advantage Index, Feeder Advantage Index, and Total Advantage Index. Producers can use the scores and indices to make selection, culling, and mating decisions. To measure the accuracy of the trait predictions, data from commercial Angus females and their progeny at the University of Missouri Thompson Research Center was utilized to analyze Weaning Weight, Milk, Marbling, Fat Thickness, Ribeye Area and Carcass Weight. Progeny phenotypic data was matched to the respective dam, and the genomic predictions were then compared to the phenotypic data using correlation and linear models in R software. Linear models accounted for differences in sex, birth year, and the random effect of sire. Interestingly, all genomic predictions had correlations with progeny phenotypes that were significantly different from zero (P-value & lt; 0.05). Likewise in the linear models, genomic predictions for all analyzed traits were significantly associated with calf performance (Table 1). Academics, farmers and ranchers, and extension professionals can trust the effectiveness of GeneMax Advantage genomic predictions in commercial Angus cattle.
    Type of Medium: Online Resource
    ISSN: 0021-8812 , 1525-3163
    URL: Article
    DOI: 10.1093/jas/skz258.173
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 1490550-4
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  • 6
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    29 Mapping Recent and Ongoing Polygenic Selection in Beef Cattle Populations
    Oxford University Press (OUP) ; 2022
    In:  Journal of Animal Science Vol. 100, No. Supplement_3 ( 2022-09-22), p. 16-16
    Details
    In: Journal of Animal Science, Oxford University Press (OUP), Vol. 100, No. Supplement_3 ( 2022-09-22), p. 16-16
    Abstract: Understanding the underlying effects of ongoing selection is of interest to livestock breeding programs. Commercial livestock genotyping has generated datasets well-suited to explore how strong artificial selection has impacted the genome over very short time periods. We have developed a method for mapping ongoing polygenic selection in populations with temporally stratified genomic data called Generation Proxy Selection Mapping (GPSM). GPSM utilizes a genome-wide linear mixed model to identify allelic associations with an animal's generation number or some proxy (i.e., birth date). We applied GPSM to two large contemporary beef cattle datasets from Red Angus (n = 46,454) and Simmental (n = 90,580) breeds, with 11,759,568 high-quality imputed variants per animal. This analysis identified 294 distinct loci actively under selection. Due to the high power of these datasets, we found that GPSM could detect very small and recent( & lt; 10 years) allele frequency changes consistent with polygenic selection. These analyses identified variants within genomic regions associated with known breed characteristics, like fertility and maternal ability in Red Angus and carcass merit and coat color in Simmental. Over 60% of GPSM loci resided in or near ( & lt; 50kb) annotated genes. We leveraged the resolution of our imputed sequence variants to overlay known epigenetic marks and possibly functional regions. 36% of GPSM loci overlapped these putatively functional regions genomic intervals. In addition to GPSM, we used two other more traditional selective sweep methods, the number of segregating loci (nSL) and Raised Accuracy in Sweep Detecting (RAiSD), to detect selection in this data. We observed minimal overlap ( & lt; 10% of loci) between traditional selective sweep mapping and GPSM. This suggests that selection mapping with GPSM can complement traditional sweep mapping methods when temporal genomic data exists. In addition to better understanding the biological processes and features that underlie artificial selection, GPSM signatures might serve as important genomic annotations.
    Type of Medium: Online Resource
    ISSN: 0021-8812 , 1525-3163
    URL: Article
    DOI: 10.1093/jas/skac247.029
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1490550-4
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  • 7
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    Genome-wide association analyses identify genotype-by-environment interactions of growth traits in Simmental cattle
    Springer Science and Business Media LLC ; 2021
    In:  Scientific Reports Vol. 11, No. 1 ( 2021-06-25)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 11, No. 1 ( 2021-06-25)
    Abstract: Understanding genotype-by-environment interactions (G × E) is crucial to understand environmental adaptation in mammals and improve the sustainability of agricultural production. Here, we present an extensive study investigating the interaction of genome-wide SNP markers with a vast assortment of environmental variables and searching for SNPs controlling phenotypic variance (vQTL) using a large beef cattle dataset. We showed that G × E contribute 10.1%, 3.8%, and 2.8% of the phenotypic variance of birth weight, weaning weight, and yearling weight, respectively. G × E genome-wide association analysis (GWAA) detected a large number of G × E loci affecting growth traits, which the traditional GWAA did not detect, showing that functional loci may have non-additive genetic effects regardless of differences in genotypic means. Further, variance-heterogeneity GWAA detected loci enriched with G × E effects without requiring prior knowledge of the interacting environmental factors. Functional annotation and pathway analysis of G × E genes revealed biological mechanisms by which cattle respond to changes in their environment, such as neurotransmitter activity, hypoxia-induced processes, keratinization, hormone, thermogenic and immune pathways. We unraveled the relevance and complexity of the genetic basis of G × E underlying growth traits, providing new insights into how different environmental conditions interact with specific genes influencing adaptation and productivity in beef cattle and potentially across mammals.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/s41598-021-92455-x
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2615211-3
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  • 8
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    De novo assembly of the cattle reference genome with single-molecule sequencing
    Oxford University Press (OUP) ; 2020
    In:  GigaScience Vol. 9, No. 3 ( 2020-03-01)
    Details
    In: GigaScience, Oxford University Press (OUP), Vol. 9, No. 3 ( 2020-03-01)
    Abstract: Major advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10–12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies. Results We present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is & gt;250× more continuous than the original assembly, with contig N50 & gt;25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use. Conclusions We demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species.
    Type of Medium: Online Resource
    ISSN: 2047-217X
    URL: Article
    DOI: 10.1093/gigascience/giaa021
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2708999-X
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  • 9
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    Feralization: Confronting the Complexity of Domestication and Evolution
    Elsevier BV ; 2021
    In:  Trends in Genetics Vol. 37, No. 4 ( 2021-04), p. 302-305
    Details
    In: Trends in Genetics, Elsevier BV, Vol. 37, No. 4 ( 2021-04), p. 302-305
    Type of Medium: Online Resource
    ISSN: 0168-9525
    URL: Article
    DOI: 10.1016/j.tig.2021.01.005
    RVK:
    WA 15000
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2021
    detail.hit.zdb_id: 2010993-3
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  • 10
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    41 Genomic Approaches to Improving Forage-based Beef Cow Efficiency
    Oxford University Press (OUP) ; 2022
    In:  Journal of Animal Science Vol. 100, No. Supplement_1 ( 2022-03-08), p. 23-24
    Details
    In: Journal of Animal Science, Oxford University Press (OUP), Vol. 100, No. Supplement_1 ( 2022-03-08), p. 23-24
    Abstract: In recent decades, the U.S. beef herd has seen massive gains in efficiency, driven by innovations in genetics, nutrition, reproduction, and resource management. Despite these advances, the industry remains under pressure to further reduce its environmental footprint. Perhaps the greatest opportunity to drive increases in sustainability is through targeted genetic improvement of forage-based cow-calf systems. While the industry has long focused on selecting for pre- and post-weaning performance, improvements in mature cow efficiency are more challenging to attain. One major impediment to directly selecting for cow efficiency is a lack of easily measured indicator phenotypes, leading some segments of the industry to focus exclusively on moderating mature size. The optimal solution to this problem will likely require a more complex understanding of the underlying biology of cow efficiency. As we consider how genomics might increase the environmental sustainability of forage-based beef production, we will need to focus on developing and measuring novel phenotypes and accounting for the complex interplay between an animal’s genetics, environment, and management. Using stochastic genetic simulations, we demonstrate the potential environmental and economic impacts of genetic selection for more efficient and well-adapted cows. We also describe possible solutions for measuring a cow’s efficiency on grass (e.g., forage intake to weaned calf pounds) that could be used to develop novel EPDs and economic selection indexes. Finally, we discuss the concept of precision genomic predictions that account for how genotypes interact with environmental stressors and management differences. We propose two potential solutions to address this concern: 1) Selecting robust cattle that perform well across all environments and management levels or 2) Developing precision predictions for precisely matching animals to their ideal production scheme.
    Type of Medium: Online Resource
    ISSN: 0021-8812 , 1525-3163
    URL: Article
    DOI: 10.1093/jas/skac028.045
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1490550-4
    SSG: 12
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